Multiple sequence alignment - TraesCS4D01G278400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G278400 chr4D 100.000 3011 0 0 1 3011 450015206 450018216 0.000000e+00 5561.0
1 TraesCS4D01G278400 chr4D 98.060 670 11 2 1 670 23217202 23216535 0.000000e+00 1164.0
2 TraesCS4D01G278400 chr4D 95.152 165 8 0 710 874 19332269 19332433 8.280000e-66 261.0
3 TraesCS4D01G278400 chr4D 83.036 112 9 5 2037 2146 449985419 449985522 3.200000e-15 93.5
4 TraesCS4D01G278400 chr4A 95.814 1314 40 6 871 2179 16959219 16957916 0.000000e+00 2108.0
5 TraesCS4D01G278400 chr4A 88.561 813 56 14 2194 3002 16956073 16955294 0.000000e+00 952.0
6 TraesCS4D01G278400 chr4A 81.867 557 73 11 2452 3002 505474694 505474160 7.660000e-121 444.0
7 TraesCS4D01G278400 chr4A 83.036 112 9 5 2037 2146 16964866 16964763 3.200000e-15 93.5
8 TraesCS4D01G278400 chr2D 98.051 667 9 2 5 670 37230444 37229781 0.000000e+00 1157.0
9 TraesCS4D01G278400 chr2D 89.516 248 26 0 2197 2444 143479342 143479095 6.270000e-82 315.0
10 TraesCS4D01G278400 chr2D 93.567 171 10 1 710 879 204046873 204047043 1.390000e-63 254.0
11 TraesCS4D01G278400 chr3D 97.349 679 17 1 1 678 208581988 208581310 0.000000e+00 1153.0
12 TraesCS4D01G278400 chr3D 85.080 563 54 12 2444 3002 247849093 247848557 5.680000e-152 547.0
13 TraesCS4D01G278400 chr3D 96.414 251 9 0 2194 2444 33204607 33204857 6.010000e-112 414.0
14 TraesCS4D01G278400 chr3D 91.111 225 20 0 2778 3002 273284115 273284339 3.770000e-79 305.0
15 TraesCS4D01G278400 chr3D 95.181 166 8 0 710 875 159789804 159789639 2.300000e-66 263.0
16 TraesCS4D01G278400 chr3D 94.479 163 9 0 710 872 486424787 486424949 4.980000e-63 252.0
17 TraesCS4D01G278400 chr3D 75.904 415 71 23 1071 1478 600179421 600179029 5.130000e-43 185.0
18 TraesCS4D01G278400 chr3A 84.413 571 58 14 2436 3002 440511792 440512335 1.590000e-147 532.0
19 TraesCS4D01G278400 chr1D 85.138 545 51 12 2462 3002 195003128 195002610 5.720000e-147 531.0
20 TraesCS4D01G278400 chr1D 84.492 561 49 16 2448 3001 274461768 274461239 1.240000e-143 520.0
21 TraesCS4D01G278400 chr5D 84.238 571 59 13 2436 3002 135287187 135287730 7.390000e-146 527.0
22 TraesCS4D01G278400 chr5D 95.092 163 8 0 710 872 488868601 488868763 1.070000e-64 257.0
23 TraesCS4D01G278400 chr6A 84.063 571 61 12 2436 3002 373043755 373044299 9.560000e-145 523.0
24 TraesCS4D01G278400 chr7B 84.014 563 61 18 2443 3002 397171147 397171683 5.760000e-142 514.0
25 TraesCS4D01G278400 chr7B 76.853 661 123 20 1336 1981 573133448 573132803 2.220000e-91 346.0
26 TraesCS4D01G278400 chr7B 73.373 999 203 49 1022 1981 626183780 626182806 2.250000e-81 313.0
27 TraesCS4D01G278400 chr7B 92.958 71 5 0 1134 1204 573140414 573140344 1.480000e-18 104.0
28 TraesCS4D01G278400 chr7A 77.791 860 158 22 1134 1981 612976362 612975524 1.610000e-137 499.0
29 TraesCS4D01G278400 chr7A 75.137 366 77 13 1020 1380 659429223 659428867 3.110000e-35 159.0
30 TraesCS4D01G278400 chr4B 83.451 568 60 16 2439 3002 188586555 188586018 5.800000e-137 497.0
31 TraesCS4D01G278400 chr4B 91.176 68 4 1 2037 2104 562712322 562712387 1.150000e-14 91.6
32 TraesCS4D01G278400 chr6B 82.771 563 83 7 2444 3002 631742994 631743546 9.700000e-135 490.0
33 TraesCS4D01G278400 chr6B 92.486 173 12 1 702 873 585530688 585530516 2.320000e-61 246.0
34 TraesCS4D01G278400 chr6B 91.111 180 15 1 701 879 648176616 648176795 3.000000e-60 243.0
35 TraesCS4D01G278400 chr3B 82.143 560 74 18 2444 3002 267906322 267906856 9.840000e-125 457.0
36 TraesCS4D01G278400 chr3B 85.673 349 27 14 2653 3001 250718287 250717962 2.220000e-91 346.0
37 TraesCS4D01G278400 chr3B 76.570 414 70 21 1071 1478 807358016 807357624 5.090000e-48 202.0
38 TraesCS4D01G278400 chr2B 94.821 251 13 0 2194 2444 110029442 110029192 2.810000e-105 392.0
39 TraesCS4D01G278400 chr2B 91.463 246 21 0 2204 2449 201449599 201449354 3.720000e-89 339.0
40 TraesCS4D01G278400 chr2B 91.286 241 21 0 2204 2444 569960413 569960653 2.240000e-86 329.0
41 TraesCS4D01G278400 chr2B 93.035 201 11 2 21 221 647373134 647372937 1.060000e-74 291.0
42 TraesCS4D01G278400 chr2B 92.655 177 11 2 707 882 214378082 214378257 1.390000e-63 254.0
43 TraesCS4D01G278400 chr5A 90.079 252 24 1 2194 2444 657224808 657224557 2.890000e-85 326.0
44 TraesCS4D01G278400 chr7D 73.791 889 166 42 1131 1981 570653393 570652534 3.800000e-74 289.0
45 TraesCS4D01G278400 chr6D 94.512 164 9 0 709 872 81746767 81746930 1.390000e-63 254.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G278400 chr4D 450015206 450018216 3010 False 5561 5561 100.0000 1 3011 1 chr4D.!!$F3 3010
1 TraesCS4D01G278400 chr4D 23216535 23217202 667 True 1164 1164 98.0600 1 670 1 chr4D.!!$R1 669
2 TraesCS4D01G278400 chr4A 16955294 16959219 3925 True 1530 2108 92.1875 871 3002 2 chr4A.!!$R3 2131
3 TraesCS4D01G278400 chr4A 505474160 505474694 534 True 444 444 81.8670 2452 3002 1 chr4A.!!$R2 550
4 TraesCS4D01G278400 chr2D 37229781 37230444 663 True 1157 1157 98.0510 5 670 1 chr2D.!!$R1 665
5 TraesCS4D01G278400 chr3D 208581310 208581988 678 True 1153 1153 97.3490 1 678 1 chr3D.!!$R2 677
6 TraesCS4D01G278400 chr3D 247848557 247849093 536 True 547 547 85.0800 2444 3002 1 chr3D.!!$R3 558
7 TraesCS4D01G278400 chr3A 440511792 440512335 543 False 532 532 84.4130 2436 3002 1 chr3A.!!$F1 566
8 TraesCS4D01G278400 chr1D 195002610 195003128 518 True 531 531 85.1380 2462 3002 1 chr1D.!!$R1 540
9 TraesCS4D01G278400 chr1D 274461239 274461768 529 True 520 520 84.4920 2448 3001 1 chr1D.!!$R2 553
10 TraesCS4D01G278400 chr5D 135287187 135287730 543 False 527 527 84.2380 2436 3002 1 chr5D.!!$F1 566
11 TraesCS4D01G278400 chr6A 373043755 373044299 544 False 523 523 84.0630 2436 3002 1 chr6A.!!$F1 566
12 TraesCS4D01G278400 chr7B 397171147 397171683 536 False 514 514 84.0140 2443 3002 1 chr7B.!!$F1 559
13 TraesCS4D01G278400 chr7B 573132803 573133448 645 True 346 346 76.8530 1336 1981 1 chr7B.!!$R1 645
14 TraesCS4D01G278400 chr7B 626182806 626183780 974 True 313 313 73.3730 1022 1981 1 chr7B.!!$R3 959
15 TraesCS4D01G278400 chr7A 612975524 612976362 838 True 499 499 77.7910 1134 1981 1 chr7A.!!$R1 847
16 TraesCS4D01G278400 chr4B 188586018 188586555 537 True 497 497 83.4510 2439 3002 1 chr4B.!!$R1 563
17 TraesCS4D01G278400 chr6B 631742994 631743546 552 False 490 490 82.7710 2444 3002 1 chr6B.!!$F1 558
18 TraesCS4D01G278400 chr3B 267906322 267906856 534 False 457 457 82.1430 2444 3002 1 chr3B.!!$F1 558
19 TraesCS4D01G278400 chr7D 570652534 570653393 859 True 289 289 73.7910 1131 1981 1 chr7D.!!$R1 850

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
986 992 0.689623 CCACAACTCAGAGAGGGCTT 59.31 55.0 3.79 0.0 33.35 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2234 0.314935 ATTGCTGGAACAAACTGCGG 59.685 50.0 0.0 0.0 38.7 5.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
670 672 2.158914 AGTCCGGTTACAAACGTTTCCT 60.159 45.455 11.37 1.61 0.00 3.36
671 673 2.613595 GTCCGGTTACAAACGTTTCCTT 59.386 45.455 11.37 0.96 0.00 3.36
672 674 3.065233 GTCCGGTTACAAACGTTTCCTTT 59.935 43.478 11.37 0.00 0.00 3.11
673 675 3.693578 TCCGGTTACAAACGTTTCCTTTT 59.306 39.130 11.37 0.00 0.00 2.27
674 676 4.157472 TCCGGTTACAAACGTTTCCTTTTT 59.843 37.500 11.37 0.00 0.00 1.94
699 701 9.522804 TTTTAATGTGTGAAAAGACCAATGTAC 57.477 29.630 0.00 0.00 0.00 2.90
700 702 5.705609 ATGTGTGAAAAGACCAATGTACC 57.294 39.130 0.00 0.00 0.00 3.34
701 703 4.787551 TGTGTGAAAAGACCAATGTACCT 58.212 39.130 0.00 0.00 0.00 3.08
702 704 5.931294 TGTGTGAAAAGACCAATGTACCTA 58.069 37.500 0.00 0.00 0.00 3.08
703 705 6.539173 TGTGTGAAAAGACCAATGTACCTAT 58.461 36.000 0.00 0.00 0.00 2.57
704 706 7.681679 TGTGTGAAAAGACCAATGTACCTATA 58.318 34.615 0.00 0.00 0.00 1.31
705 707 7.822334 TGTGTGAAAAGACCAATGTACCTATAG 59.178 37.037 0.00 0.00 0.00 1.31
706 708 7.822822 GTGTGAAAAGACCAATGTACCTATAGT 59.177 37.037 0.00 0.00 0.00 2.12
707 709 7.822334 TGTGAAAAGACCAATGTACCTATAGTG 59.178 37.037 0.00 0.00 0.00 2.74
708 710 6.821665 TGAAAAGACCAATGTACCTATAGTGC 59.178 38.462 0.00 0.00 0.00 4.40
709 711 6.561519 AAAGACCAATGTACCTATAGTGCT 57.438 37.500 0.00 0.00 31.32 4.40
710 712 7.670605 AAAGACCAATGTACCTATAGTGCTA 57.329 36.000 0.00 0.00 31.32 3.49
711 713 6.651975 AGACCAATGTACCTATAGTGCTAC 57.348 41.667 0.00 0.00 31.32 3.58
712 714 6.374588 AGACCAATGTACCTATAGTGCTACT 58.625 40.000 0.00 0.00 31.32 2.57
713 715 6.490721 AGACCAATGTACCTATAGTGCTACTC 59.509 42.308 0.00 0.00 31.32 2.59
714 716 5.539193 ACCAATGTACCTATAGTGCTACTCC 59.461 44.000 0.00 0.00 31.32 3.85
715 717 5.047235 CCAATGTACCTATAGTGCTACTCCC 60.047 48.000 0.00 0.00 31.32 4.30
716 718 5.602291 ATGTACCTATAGTGCTACTCCCT 57.398 43.478 0.00 0.00 31.32 4.20
717 719 4.983053 TGTACCTATAGTGCTACTCCCTC 58.017 47.826 0.00 0.00 31.32 4.30
718 720 3.529216 ACCTATAGTGCTACTCCCTCC 57.471 52.381 0.00 0.00 0.00 4.30
719 721 2.224818 ACCTATAGTGCTACTCCCTCCG 60.225 54.545 0.00 0.00 0.00 4.63
720 722 2.224818 CCTATAGTGCTACTCCCTCCGT 60.225 54.545 0.00 0.00 0.00 4.69
721 723 2.456073 ATAGTGCTACTCCCTCCGTT 57.544 50.000 0.00 0.00 0.00 4.44
722 724 2.226962 TAGTGCTACTCCCTCCGTTT 57.773 50.000 0.00 0.00 0.00 3.60
723 725 0.896226 AGTGCTACTCCCTCCGTTTC 59.104 55.000 0.00 0.00 0.00 2.78
724 726 0.896226 GTGCTACTCCCTCCGTTTCT 59.104 55.000 0.00 0.00 0.00 2.52
725 727 2.097825 GTGCTACTCCCTCCGTTTCTA 58.902 52.381 0.00 0.00 0.00 2.10
726 728 2.494870 GTGCTACTCCCTCCGTTTCTAA 59.505 50.000 0.00 0.00 0.00 2.10
727 729 3.056322 GTGCTACTCCCTCCGTTTCTAAA 60.056 47.826 0.00 0.00 0.00 1.85
728 730 3.773119 TGCTACTCCCTCCGTTTCTAAAT 59.227 43.478 0.00 0.00 0.00 1.40
729 731 4.957954 TGCTACTCCCTCCGTTTCTAAATA 59.042 41.667 0.00 0.00 0.00 1.40
730 732 5.601313 TGCTACTCCCTCCGTTTCTAAATAT 59.399 40.000 0.00 0.00 0.00 1.28
731 733 6.779049 TGCTACTCCCTCCGTTTCTAAATATA 59.221 38.462 0.00 0.00 0.00 0.86
732 734 7.288389 TGCTACTCCCTCCGTTTCTAAATATAA 59.712 37.037 0.00 0.00 0.00 0.98
733 735 7.813627 GCTACTCCCTCCGTTTCTAAATATAAG 59.186 40.741 0.00 0.00 0.00 1.73
734 736 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
735 737 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
736 738 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
737 739 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
738 740 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
739 741 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
740 742 9.379791 CCTCCGTTTCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
758 760 9.014297 AGTCTTTGTAAAGATTTCATTAGGTGG 57.986 33.333 9.98 0.00 45.83 4.61
759 761 9.010029 GTCTTTGTAAAGATTTCATTAGGTGGA 57.990 33.333 9.98 0.00 45.83 4.02
760 762 9.010029 TCTTTGTAAAGATTTCATTAGGTGGAC 57.990 33.333 3.05 0.00 39.95 4.02
761 763 8.934023 TTTGTAAAGATTTCATTAGGTGGACT 57.066 30.769 0.00 0.00 0.00 3.85
763 765 9.444600 TTGTAAAGATTTCATTAGGTGGACTAC 57.555 33.333 0.00 0.00 0.00 2.73
764 766 8.598916 TGTAAAGATTTCATTAGGTGGACTACA 58.401 33.333 0.00 0.00 0.00 2.74
765 767 9.614792 GTAAAGATTTCATTAGGTGGACTACAT 57.385 33.333 0.00 0.00 0.00 2.29
767 769 9.614792 AAAGATTTCATTAGGTGGACTACATAC 57.385 33.333 0.00 0.00 0.00 2.39
768 770 7.434492 AGATTTCATTAGGTGGACTACATACG 58.566 38.462 0.00 0.00 0.00 3.06
769 771 5.524971 TTCATTAGGTGGACTACATACGG 57.475 43.478 0.00 0.00 0.00 4.02
770 772 4.795469 TCATTAGGTGGACTACATACGGA 58.205 43.478 0.00 0.00 0.00 4.69
771 773 4.825634 TCATTAGGTGGACTACATACGGAG 59.174 45.833 0.00 0.00 0.00 4.63
772 774 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
773 775 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
774 776 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
775 777 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
776 778 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
777 779 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
778 780 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
779 781 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
780 782 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
781 783 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
782 784 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
783 785 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
784 786 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
785 787 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
786 788 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
787 789 4.376340 ACGGAGCAAAATGAATGAATCC 57.624 40.909 0.00 0.00 0.00 3.01
788 790 3.763360 ACGGAGCAAAATGAATGAATCCA 59.237 39.130 0.00 0.00 0.00 3.41
789 791 4.107622 CGGAGCAAAATGAATGAATCCAC 58.892 43.478 0.00 0.00 0.00 4.02
790 792 4.380761 CGGAGCAAAATGAATGAATCCACA 60.381 41.667 0.00 0.00 0.00 4.17
791 793 4.866486 GGAGCAAAATGAATGAATCCACAC 59.134 41.667 0.00 0.00 0.00 3.82
792 794 5.337009 GGAGCAAAATGAATGAATCCACACT 60.337 40.000 0.00 0.00 0.00 3.55
793 795 6.105397 AGCAAAATGAATGAATCCACACTT 57.895 33.333 0.00 0.00 0.00 3.16
794 796 7.230849 AGCAAAATGAATGAATCCACACTTA 57.769 32.000 0.00 0.00 0.00 2.24
795 797 7.669427 AGCAAAATGAATGAATCCACACTTAA 58.331 30.769 0.00 0.00 0.00 1.85
796 798 8.149647 AGCAAAATGAATGAATCCACACTTAAA 58.850 29.630 0.00 0.00 0.00 1.52
797 799 8.772705 GCAAAATGAATGAATCCACACTTAAAA 58.227 29.630 0.00 0.00 0.00 1.52
800 802 8.483307 AATGAATGAATCCACACTTAAAATGC 57.517 30.769 0.00 0.00 0.00 3.56
801 803 6.990798 TGAATGAATCCACACTTAAAATGCA 58.009 32.000 0.00 0.00 0.00 3.96
802 804 7.613585 TGAATGAATCCACACTTAAAATGCAT 58.386 30.769 0.00 0.00 0.00 3.96
803 805 7.760794 TGAATGAATCCACACTTAAAATGCATC 59.239 33.333 0.00 0.00 0.00 3.91
804 806 6.839124 TGAATCCACACTTAAAATGCATCT 57.161 33.333 0.00 0.00 0.00 2.90
805 807 7.936496 TGAATCCACACTTAAAATGCATCTA 57.064 32.000 0.00 0.00 0.00 1.98
806 808 7.761409 TGAATCCACACTTAAAATGCATCTAC 58.239 34.615 0.00 0.00 0.00 2.59
807 809 7.392953 TGAATCCACACTTAAAATGCATCTACA 59.607 33.333 0.00 0.00 0.00 2.74
808 810 7.886629 ATCCACACTTAAAATGCATCTACAT 57.113 32.000 0.00 0.00 0.00 2.29
809 811 8.978874 ATCCACACTTAAAATGCATCTACATA 57.021 30.769 0.00 0.00 0.00 2.29
810 812 8.208718 TCCACACTTAAAATGCATCTACATAC 57.791 34.615 0.00 0.00 0.00 2.39
811 813 7.826744 TCCACACTTAAAATGCATCTACATACA 59.173 33.333 0.00 0.00 0.00 2.29
812 814 8.623903 CCACACTTAAAATGCATCTACATACAT 58.376 33.333 0.00 0.00 0.00 2.29
813 815 9.655769 CACACTTAAAATGCATCTACATACATC 57.344 33.333 0.00 0.00 0.00 3.06
814 816 8.840321 ACACTTAAAATGCATCTACATACATCC 58.160 33.333 0.00 0.00 0.00 3.51
815 817 8.011673 CACTTAAAATGCATCTACATACATCCG 58.988 37.037 0.00 0.00 0.00 4.18
816 818 7.715249 ACTTAAAATGCATCTACATACATCCGT 59.285 33.333 0.00 0.00 0.00 4.69
817 819 9.203421 CTTAAAATGCATCTACATACATCCGTA 57.797 33.333 0.00 0.00 0.00 4.02
818 820 9.719355 TTAAAATGCATCTACATACATCCGTAT 57.281 29.630 0.00 0.00 38.96 3.06
831 833 4.795268 ACATCCGTATGTAGTTCATAGCG 58.205 43.478 0.00 0.00 44.66 4.26
832 834 4.517832 ACATCCGTATGTAGTTCATAGCGA 59.482 41.667 0.00 2.52 44.66 4.93
833 835 5.009310 ACATCCGTATGTAGTTCATAGCGAA 59.991 40.000 0.00 0.00 44.66 4.70
834 836 5.503662 TCCGTATGTAGTTCATAGCGAAA 57.496 39.130 10.82 1.34 39.36 3.46
835 837 6.080648 TCCGTATGTAGTTCATAGCGAAAT 57.919 37.500 10.82 0.00 39.36 2.17
836 838 6.147581 TCCGTATGTAGTTCATAGCGAAATC 58.852 40.000 10.82 0.00 39.36 2.17
837 839 6.016527 TCCGTATGTAGTTCATAGCGAAATCT 60.017 38.462 10.82 0.00 39.36 2.40
838 840 6.305877 CCGTATGTAGTTCATAGCGAAATCTC 59.694 42.308 10.82 0.00 39.36 2.75
839 841 7.078851 CGTATGTAGTTCATAGCGAAATCTCT 58.921 38.462 0.00 0.00 39.36 3.10
840 842 8.228464 CGTATGTAGTTCATAGCGAAATCTCTA 58.772 37.037 0.00 0.00 39.36 2.43
841 843 9.332301 GTATGTAGTTCATAGCGAAATCTCTAC 57.668 37.037 0.00 0.00 39.36 2.59
842 844 7.329588 TGTAGTTCATAGCGAAATCTCTACA 57.670 36.000 0.00 0.00 37.24 2.74
843 845 7.768240 TGTAGTTCATAGCGAAATCTCTACAA 58.232 34.615 0.00 0.00 36.92 2.41
844 846 8.248253 TGTAGTTCATAGCGAAATCTCTACAAA 58.752 33.333 0.00 0.00 36.92 2.83
845 847 7.763172 AGTTCATAGCGAAATCTCTACAAAG 57.237 36.000 0.00 0.00 34.69 2.77
846 848 7.548097 AGTTCATAGCGAAATCTCTACAAAGA 58.452 34.615 0.00 0.00 34.69 2.52
847 849 8.200792 AGTTCATAGCGAAATCTCTACAAAGAT 58.799 33.333 0.00 0.00 37.61 2.40
848 850 8.821894 GTTCATAGCGAAATCTCTACAAAGATT 58.178 33.333 0.00 0.00 45.67 2.40
866 868 9.338622 ACAAAGATTTATATTTAGGAACGGAGG 57.661 33.333 0.00 0.00 0.00 4.30
867 869 9.555727 CAAAGATTTATATTTAGGAACGGAGGA 57.444 33.333 0.00 0.00 0.00 3.71
869 871 9.780186 AAGATTTATATTTAGGAACGGAGGAAG 57.220 33.333 0.00 0.00 0.00 3.46
906 908 1.668337 CGGCAGAGCTCCATCGATTAG 60.668 57.143 10.93 0.00 0.00 1.73
908 910 2.609244 GGCAGAGCTCCATCGATTAGTC 60.609 54.545 10.93 0.00 0.00 2.59
959 965 3.614659 CGAGAGAGCGCATGCACG 61.615 66.667 19.57 6.02 46.23 5.34
973 979 1.098712 TGCACGAGGAAACCCACAAC 61.099 55.000 0.00 0.00 0.00 3.32
985 991 1.197430 CCCACAACTCAGAGAGGGCT 61.197 60.000 3.79 0.00 33.35 5.19
986 992 0.689623 CCACAACTCAGAGAGGGCTT 59.310 55.000 3.79 0.00 33.35 4.35
998 1004 4.221703 CAGAGAGGGCTTCACGGATATATT 59.778 45.833 0.00 0.00 0.00 1.28
1008 1014 6.034683 GCTTCACGGATATATTAATGTCGTCC 59.965 42.308 0.00 2.77 0.00 4.79
1011 1017 5.737757 CACGGATATATTAATGTCGTCCTCG 59.262 44.000 11.97 5.48 38.55 4.63
1018 1024 2.414994 AATGTCGTCCTCGTCTCCTA 57.585 50.000 0.00 0.00 38.33 2.94
1120 1126 2.978010 CGCCACCACTCCAACCAC 60.978 66.667 0.00 0.00 0.00 4.16
1272 1281 0.179078 TTGTGTACTTTCACGGCGGT 60.179 50.000 13.24 0.64 40.74 5.68
1617 1656 3.564218 ATCCTCCTCATGCCGGGC 61.564 66.667 13.32 13.32 0.00 6.13
1647 1686 0.601046 CTGAGCCAACGCAGTCAGAA 60.601 55.000 0.00 0.00 45.00 3.02
1648 1687 0.035317 TGAGCCAACGCAGTCAGAAT 59.965 50.000 0.00 0.00 45.00 2.40
2001 2052 3.148279 GAGCGGGATGGAGACGGT 61.148 66.667 0.00 0.00 41.36 4.83
2064 2116 2.814336 GTTTGTTCCCGCATTTCTCTCT 59.186 45.455 0.00 0.00 0.00 3.10
2065 2117 2.386661 TGTTCCCGCATTTCTCTCTC 57.613 50.000 0.00 0.00 0.00 3.20
2066 2118 1.902508 TGTTCCCGCATTTCTCTCTCT 59.097 47.619 0.00 0.00 0.00 3.10
2078 2130 6.540189 GCATTTCTCTCTCTAACCTTTGCATA 59.460 38.462 0.00 0.00 0.00 3.14
2100 2152 3.572642 TGGTGAGAGGTTGAGTGACTTA 58.427 45.455 0.00 0.00 0.00 2.24
2101 2153 3.964688 TGGTGAGAGGTTGAGTGACTTAA 59.035 43.478 0.00 0.00 0.00 1.85
2102 2154 4.039245 TGGTGAGAGGTTGAGTGACTTAAG 59.961 45.833 0.00 0.00 0.00 1.85
2103 2155 3.991121 GTGAGAGGTTGAGTGACTTAAGC 59.009 47.826 10.81 10.81 0.00 3.09
2104 2156 3.898123 TGAGAGGTTGAGTGACTTAAGCT 59.102 43.478 19.62 19.62 39.76 3.74
2105 2157 4.241681 GAGAGGTTGAGTGACTTAAGCTG 58.758 47.826 23.56 0.00 37.79 4.24
2106 2158 3.643792 AGAGGTTGAGTGACTTAAGCTGT 59.356 43.478 23.56 17.80 37.79 4.40
2107 2159 4.101741 AGAGGTTGAGTGACTTAAGCTGTT 59.898 41.667 23.56 10.77 37.79 3.16
2108 2160 5.304614 AGAGGTTGAGTGACTTAAGCTGTTA 59.695 40.000 23.56 0.00 37.79 2.41
2139 2191 1.132262 ACGTTGCCATGGCGAATAAAG 59.868 47.619 28.68 21.10 45.51 1.85
2160 2212 1.273048 ACGGCATAGTTCACGTTACCA 59.727 47.619 0.00 0.00 35.90 3.25
2179 2231 4.360889 ACCATTGGGCAAGGAATAATTGA 58.639 39.130 7.78 0.00 37.90 2.57
2180 2232 4.406649 ACCATTGGGCAAGGAATAATTGAG 59.593 41.667 7.78 0.00 37.90 3.02
2181 2233 4.374399 CATTGGGCAAGGAATAATTGAGC 58.626 43.478 0.00 0.00 0.00 4.26
2182 2234 2.387757 TGGGCAAGGAATAATTGAGCC 58.612 47.619 0.00 0.00 39.86 4.70
2184 2236 1.338020 GGCAAGGAATAATTGAGCCCG 59.662 52.381 0.00 0.00 34.71 6.13
2185 2237 1.269257 GCAAGGAATAATTGAGCCCGC 60.269 52.381 0.00 0.00 0.00 6.13
2186 2238 2.023673 CAAGGAATAATTGAGCCCGCA 58.976 47.619 0.00 0.00 0.00 5.69
2187 2239 1.972872 AGGAATAATTGAGCCCGCAG 58.027 50.000 0.00 0.00 0.00 5.18
2188 2240 1.212935 AGGAATAATTGAGCCCGCAGT 59.787 47.619 0.00 0.00 0.00 4.40
2192 2244 1.904287 TAATTGAGCCCGCAGTTTGT 58.096 45.000 0.00 0.00 0.00 2.83
2202 4082 1.269726 CCGCAGTTTGTTCCAGCAATT 60.270 47.619 0.00 0.00 0.00 2.32
2274 4154 0.246086 TTGAATGTTTGGATGCCGGC 59.754 50.000 22.73 22.73 0.00 6.13
2286 4166 1.071699 GATGCCGGCCCAAATACTCTA 59.928 52.381 26.77 0.00 0.00 2.43
2318 4198 2.930826 TGACCCCTTCTTCAGTTGAC 57.069 50.000 0.00 0.00 0.00 3.18
2320 4200 2.104792 TGACCCCTTCTTCAGTTGACAG 59.895 50.000 0.00 0.00 0.00 3.51
2336 4216 6.146837 CAGTTGACAGTTTAAGATGTCTCCTG 59.853 42.308 17.82 17.39 44.90 3.86
2338 4218 6.911250 TGACAGTTTAAGATGTCTCCTGTA 57.089 37.500 17.82 0.85 44.90 2.74
2361 4241 5.742063 AGGGTAATACCTTGCTCTTAACAC 58.258 41.667 9.58 0.00 37.69 3.32
2363 4243 5.816258 GGGTAATACCTTGCTCTTAACACTC 59.184 44.000 9.58 0.00 38.64 3.51
2367 4247 1.461127 CCTTGCTCTTAACACTCGTGC 59.539 52.381 0.00 0.00 0.00 5.34
2421 4301 1.417145 ACATTGCTTGGCCAACATTGT 59.583 42.857 25.88 25.88 0.00 2.71
2523 4403 7.400599 TCTATTCGTATGTATATCCCACACC 57.599 40.000 0.00 0.00 0.00 4.16
2531 4411 5.168647 TGTATATCCCACACCGTTTTCTT 57.831 39.130 0.00 0.00 0.00 2.52
2533 4413 6.005198 TGTATATCCCACACCGTTTTCTTTT 58.995 36.000 0.00 0.00 0.00 2.27
2557 4437 0.656495 CTCGTGCGCGATACGTGTAT 60.656 55.000 24.28 0.00 46.80 2.29
2616 4497 8.888716 TGCTTTATTCAAATATATCACACACGT 58.111 29.630 0.00 0.00 0.00 4.49
2680 4562 4.031426 CACGCTTTTACTGATAGAACCGTC 59.969 45.833 0.00 0.00 0.00 4.79
2767 4678 9.669353 GCAAATTCACATTTCATATCGAATAGT 57.331 29.630 0.00 0.00 32.32 2.12
2773 4684 9.986833 TCACATTTCATATCGAATAGTTGTTTG 57.013 29.630 0.00 0.00 32.32 2.93
2774 4685 8.736742 CACATTTCATATCGAATAGTTGTTTGC 58.263 33.333 0.00 0.00 32.32 3.68
2775 4686 7.915397 ACATTTCATATCGAATAGTTGTTTGCC 59.085 33.333 0.00 0.00 32.32 4.52
2776 4687 6.993786 TTCATATCGAATAGTTGTTTGCCA 57.006 33.333 0.00 0.00 0.00 4.92
2777 4688 6.993786 TCATATCGAATAGTTGTTTGCCAA 57.006 33.333 0.00 0.00 0.00 4.52
2778 4689 7.566760 TCATATCGAATAGTTGTTTGCCAAT 57.433 32.000 0.00 0.00 35.02 3.16
2779 4690 7.995289 TCATATCGAATAGTTGTTTGCCAATT 58.005 30.769 0.00 0.00 35.02 2.32
2780 4691 8.465999 TCATATCGAATAGTTGTTTGCCAATTT 58.534 29.630 0.00 0.00 35.02 1.82
2781 4692 8.745837 CATATCGAATAGTTGTTTGCCAATTTC 58.254 33.333 0.00 0.00 35.02 2.17
2782 4693 6.078202 TCGAATAGTTGTTTGCCAATTTCA 57.922 33.333 0.00 0.00 35.02 2.69
2783 4694 6.686630 TCGAATAGTTGTTTGCCAATTTCAT 58.313 32.000 0.00 0.00 35.02 2.57
2784 4695 7.821652 TCGAATAGTTGTTTGCCAATTTCATA 58.178 30.769 0.00 0.00 35.02 2.15
2785 4696 8.465999 TCGAATAGTTGTTTGCCAATTTCATAT 58.534 29.630 0.00 0.00 35.02 1.78
2786 4697 8.745837 CGAATAGTTGTTTGCCAATTTCATATC 58.254 33.333 0.00 0.00 35.02 1.63
2787 4698 8.633075 AATAGTTGTTTGCCAATTTCATATCG 57.367 30.769 0.00 0.00 35.02 2.92
2788 4699 6.266168 AGTTGTTTGCCAATTTCATATCGA 57.734 33.333 0.00 0.00 35.02 3.59
2789 4700 6.686630 AGTTGTTTGCCAATTTCATATCGAA 58.313 32.000 0.00 0.00 35.02 3.71
2790 4701 7.322664 AGTTGTTTGCCAATTTCATATCGAAT 58.677 30.769 0.00 0.00 35.02 3.34
2791 4702 8.465999 AGTTGTTTGCCAATTTCATATCGAATA 58.534 29.630 0.00 0.00 35.02 1.75
2792 4703 9.081997 GTTGTTTGCCAATTTCATATCGAATAA 57.918 29.630 0.00 0.00 35.02 1.40
2826 4764 9.630098 CCAATTTCATATCAGGCACATAAATAC 57.370 33.333 0.00 0.00 0.00 1.89
2955 4893 0.520404 CGGATGCATGATTAGCCAGC 59.480 55.000 2.46 0.00 0.00 4.85
3005 4943 5.828299 TCAGTAAGAACCTGTTTTGTTGG 57.172 39.130 0.00 0.00 0.00 3.77
3006 4944 4.642885 TCAGTAAGAACCTGTTTTGTTGGG 59.357 41.667 0.00 0.00 0.00 4.12
3007 4945 3.958147 AGTAAGAACCTGTTTTGTTGGGG 59.042 43.478 0.00 0.00 0.00 4.96
3008 4946 2.838637 AGAACCTGTTTTGTTGGGGA 57.161 45.000 0.00 0.00 0.00 4.81
3009 4947 3.328535 AGAACCTGTTTTGTTGGGGAT 57.671 42.857 0.00 0.00 0.00 3.85
3010 4948 4.463050 AGAACCTGTTTTGTTGGGGATA 57.537 40.909 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 0.815734 ACTGCTATGACTACGGCGTT 59.184 50.000 21.24 0.00 0.00 4.84
673 675 9.522804 GTACATTGGTCTTTTCACACATTAAAA 57.477 29.630 0.00 0.00 0.00 1.52
674 676 8.138712 GGTACATTGGTCTTTTCACACATTAAA 58.861 33.333 0.00 0.00 0.00 1.52
675 677 7.504238 AGGTACATTGGTCTTTTCACACATTAA 59.496 33.333 0.00 0.00 0.00 1.40
676 678 7.001674 AGGTACATTGGTCTTTTCACACATTA 58.998 34.615 0.00 0.00 0.00 1.90
677 679 5.833131 AGGTACATTGGTCTTTTCACACATT 59.167 36.000 0.00 0.00 0.00 2.71
678 680 5.385198 AGGTACATTGGTCTTTTCACACAT 58.615 37.500 0.00 0.00 0.00 3.21
679 681 4.787551 AGGTACATTGGTCTTTTCACACA 58.212 39.130 0.00 0.00 0.00 3.72
680 682 7.822822 ACTATAGGTACATTGGTCTTTTCACAC 59.177 37.037 4.43 0.00 0.00 3.82
681 683 7.822334 CACTATAGGTACATTGGTCTTTTCACA 59.178 37.037 4.43 0.00 0.00 3.58
682 684 7.201617 GCACTATAGGTACATTGGTCTTTTCAC 60.202 40.741 4.43 0.00 0.00 3.18
683 685 6.821665 GCACTATAGGTACATTGGTCTTTTCA 59.178 38.462 4.43 0.00 0.00 2.69
684 686 7.048512 AGCACTATAGGTACATTGGTCTTTTC 58.951 38.462 4.43 0.00 0.00 2.29
685 687 6.958767 AGCACTATAGGTACATTGGTCTTTT 58.041 36.000 4.43 0.00 0.00 2.27
686 688 6.561519 AGCACTATAGGTACATTGGTCTTT 57.438 37.500 4.43 0.00 0.00 2.52
687 689 6.839657 AGTAGCACTATAGGTACATTGGTCTT 59.160 38.462 4.43 0.00 43.13 3.01
688 690 6.374588 AGTAGCACTATAGGTACATTGGTCT 58.625 40.000 4.43 0.00 43.13 3.85
689 691 6.294620 GGAGTAGCACTATAGGTACATTGGTC 60.295 46.154 4.43 0.00 43.13 4.02
690 692 5.539193 GGAGTAGCACTATAGGTACATTGGT 59.461 44.000 4.43 0.46 43.13 3.67
691 693 5.047235 GGGAGTAGCACTATAGGTACATTGG 60.047 48.000 4.43 0.00 43.13 3.16
692 694 5.775701 AGGGAGTAGCACTATAGGTACATTG 59.224 44.000 4.43 0.00 43.13 2.82
693 695 5.966684 AGGGAGTAGCACTATAGGTACATT 58.033 41.667 4.43 0.00 43.13 2.71
694 696 5.516945 GGAGGGAGTAGCACTATAGGTACAT 60.517 48.000 4.43 0.00 43.13 2.29
695 697 4.202545 GGAGGGAGTAGCACTATAGGTACA 60.203 50.000 4.43 0.00 43.13 2.90
696 698 4.334552 GGAGGGAGTAGCACTATAGGTAC 58.665 52.174 4.43 3.24 41.51 3.34
697 699 3.008813 CGGAGGGAGTAGCACTATAGGTA 59.991 52.174 4.43 0.00 0.00 3.08
698 700 2.224818 CGGAGGGAGTAGCACTATAGGT 60.225 54.545 4.43 0.00 0.00 3.08
699 701 2.224818 ACGGAGGGAGTAGCACTATAGG 60.225 54.545 4.43 0.00 0.00 2.57
700 702 3.143211 ACGGAGGGAGTAGCACTATAG 57.857 52.381 0.00 0.00 0.00 1.31
701 703 3.589951 AACGGAGGGAGTAGCACTATA 57.410 47.619 0.00 0.00 0.00 1.31
702 704 2.456073 AACGGAGGGAGTAGCACTAT 57.544 50.000 0.00 0.00 0.00 2.12
703 705 2.097825 GAAACGGAGGGAGTAGCACTA 58.902 52.381 0.00 0.00 0.00 2.74
704 706 0.896226 GAAACGGAGGGAGTAGCACT 59.104 55.000 0.00 0.00 0.00 4.40
705 707 0.896226 AGAAACGGAGGGAGTAGCAC 59.104 55.000 0.00 0.00 0.00 4.40
706 708 2.519771 TAGAAACGGAGGGAGTAGCA 57.480 50.000 0.00 0.00 0.00 3.49
707 709 3.881937 TTTAGAAACGGAGGGAGTAGC 57.118 47.619 0.00 0.00 0.00 3.58
708 710 8.858094 ACTTATATTTAGAAACGGAGGGAGTAG 58.142 37.037 0.00 0.00 0.00 2.57
709 711 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
710 712 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
711 713 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
712 714 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
713 715 8.827677 CAAAGACTTATATTTAGAAACGGAGGG 58.172 37.037 0.00 0.00 0.00 4.30
714 716 9.379791 ACAAAGACTTATATTTAGAAACGGAGG 57.620 33.333 0.00 0.00 0.00 4.30
732 734 9.014297 CCACCTAATGAAATCTTTACAAAGACT 57.986 33.333 6.56 0.00 46.80 3.24
733 735 9.010029 TCCACCTAATGAAATCTTTACAAAGAC 57.990 33.333 6.56 0.00 46.80 3.01
735 737 9.014297 AGTCCACCTAATGAAATCTTTACAAAG 57.986 33.333 0.00 0.00 37.36 2.77
736 738 8.934023 AGTCCACCTAATGAAATCTTTACAAA 57.066 30.769 0.00 0.00 0.00 2.83
737 739 9.444600 GTAGTCCACCTAATGAAATCTTTACAA 57.555 33.333 0.00 0.00 0.00 2.41
738 740 8.598916 TGTAGTCCACCTAATGAAATCTTTACA 58.401 33.333 0.00 0.00 0.00 2.41
739 741 9.614792 ATGTAGTCCACCTAATGAAATCTTTAC 57.385 33.333 0.00 0.00 0.00 2.01
741 743 9.614792 GTATGTAGTCCACCTAATGAAATCTTT 57.385 33.333 0.00 0.00 0.00 2.52
742 744 7.926555 CGTATGTAGTCCACCTAATGAAATCTT 59.073 37.037 0.00 0.00 0.00 2.40
743 745 7.434492 CGTATGTAGTCCACCTAATGAAATCT 58.566 38.462 0.00 0.00 0.00 2.40
744 746 6.645415 CCGTATGTAGTCCACCTAATGAAATC 59.355 42.308 0.00 0.00 0.00 2.17
745 747 6.325545 TCCGTATGTAGTCCACCTAATGAAAT 59.674 38.462 0.00 0.00 0.00 2.17
746 748 5.657745 TCCGTATGTAGTCCACCTAATGAAA 59.342 40.000 0.00 0.00 0.00 2.69
747 749 5.202765 TCCGTATGTAGTCCACCTAATGAA 58.797 41.667 0.00 0.00 0.00 2.57
748 750 4.795469 TCCGTATGTAGTCCACCTAATGA 58.205 43.478 0.00 0.00 0.00 2.57
749 751 4.558898 GCTCCGTATGTAGTCCACCTAATG 60.559 50.000 0.00 0.00 0.00 1.90
750 752 3.573110 GCTCCGTATGTAGTCCACCTAAT 59.427 47.826 0.00 0.00 0.00 1.73
751 753 2.954318 GCTCCGTATGTAGTCCACCTAA 59.046 50.000 0.00 0.00 0.00 2.69
752 754 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
753 755 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
754 756 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
755 757 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
756 758 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
757 759 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
758 760 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
759 761 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
760 762 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
761 763 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
762 764 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
763 765 5.916883 GGATTCATTCATTTTGCTCCGTATG 59.083 40.000 0.00 0.00 0.00 2.39
764 766 5.593909 TGGATTCATTCATTTTGCTCCGTAT 59.406 36.000 0.00 0.00 0.00 3.06
765 767 4.946772 TGGATTCATTCATTTTGCTCCGTA 59.053 37.500 0.00 0.00 0.00 4.02
766 768 3.763360 TGGATTCATTCATTTTGCTCCGT 59.237 39.130 0.00 0.00 0.00 4.69
767 769 4.107622 GTGGATTCATTCATTTTGCTCCG 58.892 43.478 0.00 0.00 0.00 4.63
768 770 4.866486 GTGTGGATTCATTCATTTTGCTCC 59.134 41.667 0.00 0.00 0.00 4.70
769 771 5.717119 AGTGTGGATTCATTCATTTTGCTC 58.283 37.500 0.00 0.00 0.00 4.26
770 772 5.733620 AGTGTGGATTCATTCATTTTGCT 57.266 34.783 0.00 0.00 0.00 3.91
771 773 7.887996 TTAAGTGTGGATTCATTCATTTTGC 57.112 32.000 0.00 0.00 0.00 3.68
774 776 8.938906 GCATTTTAAGTGTGGATTCATTCATTT 58.061 29.630 0.00 0.00 0.00 2.32
775 777 8.095792 TGCATTTTAAGTGTGGATTCATTCATT 58.904 29.630 0.00 0.00 0.00 2.57
776 778 7.613585 TGCATTTTAAGTGTGGATTCATTCAT 58.386 30.769 0.00 0.00 0.00 2.57
777 779 6.990798 TGCATTTTAAGTGTGGATTCATTCA 58.009 32.000 0.00 0.00 0.00 2.57
778 780 7.977853 AGATGCATTTTAAGTGTGGATTCATTC 59.022 33.333 0.00 0.00 0.00 2.67
779 781 7.844009 AGATGCATTTTAAGTGTGGATTCATT 58.156 30.769 0.00 0.00 0.00 2.57
780 782 7.414222 AGATGCATTTTAAGTGTGGATTCAT 57.586 32.000 0.00 0.00 0.00 2.57
781 783 6.839124 AGATGCATTTTAAGTGTGGATTCA 57.161 33.333 0.00 0.00 0.00 2.57
782 784 7.761409 TGTAGATGCATTTTAAGTGTGGATTC 58.239 34.615 0.00 0.00 0.00 2.52
783 785 7.701539 TGTAGATGCATTTTAAGTGTGGATT 57.298 32.000 0.00 0.00 0.00 3.01
784 786 7.886629 ATGTAGATGCATTTTAAGTGTGGAT 57.113 32.000 0.00 0.00 0.00 3.41
785 787 7.826744 TGTATGTAGATGCATTTTAAGTGTGGA 59.173 33.333 0.00 0.00 0.00 4.02
786 788 7.984391 TGTATGTAGATGCATTTTAAGTGTGG 58.016 34.615 0.00 0.00 0.00 4.17
787 789 9.655769 GATGTATGTAGATGCATTTTAAGTGTG 57.344 33.333 0.00 0.00 35.26 3.82
788 790 8.840321 GGATGTATGTAGATGCATTTTAAGTGT 58.160 33.333 0.00 0.00 35.26 3.55
789 791 8.011673 CGGATGTATGTAGATGCATTTTAAGTG 58.988 37.037 0.00 0.00 35.26 3.16
790 792 7.715249 ACGGATGTATGTAGATGCATTTTAAGT 59.285 33.333 0.00 0.14 35.26 2.24
791 793 8.087982 ACGGATGTATGTAGATGCATTTTAAG 57.912 34.615 0.00 0.00 35.26 1.85
792 794 9.719355 ATACGGATGTATGTAGATGCATTTTAA 57.281 29.630 0.00 0.00 39.81 1.52
807 809 6.373495 TCGCTATGAACTACATACGGATGTAT 59.627 38.462 20.64 7.28 45.42 2.29
808 810 5.702209 TCGCTATGAACTACATACGGATGTA 59.298 40.000 19.32 19.32 44.77 2.29
809 811 6.460537 TTTCGCTATGAACTACATACGGATGT 60.461 38.462 19.12 19.12 42.00 3.06
810 812 5.043189 TCGCTATGAACTACATACGGATG 57.957 43.478 5.94 5.94 40.07 3.51
811 813 5.700722 TTCGCTATGAACTACATACGGAT 57.299 39.130 0.00 0.00 40.07 4.18
812 814 5.503662 TTTCGCTATGAACTACATACGGA 57.496 39.130 0.00 0.00 40.07 4.69
813 815 6.150318 AGATTTCGCTATGAACTACATACGG 58.850 40.000 0.00 0.00 40.07 4.02
814 816 7.078851 AGAGATTTCGCTATGAACTACATACG 58.921 38.462 0.00 0.00 40.07 3.06
815 817 9.332301 GTAGAGATTTCGCTATGAACTACATAC 57.668 37.037 0.00 0.00 40.07 2.39
816 818 9.063615 TGTAGAGATTTCGCTATGAACTACATA 57.936 33.333 0.00 0.00 37.45 2.29
817 819 7.941919 TGTAGAGATTTCGCTATGAACTACAT 58.058 34.615 0.00 0.00 37.45 2.29
818 820 7.329588 TGTAGAGATTTCGCTATGAACTACA 57.670 36.000 0.00 0.00 38.81 2.74
819 821 8.630278 TTTGTAGAGATTTCGCTATGAACTAC 57.370 34.615 0.00 0.00 35.97 2.73
820 822 8.683615 TCTTTGTAGAGATTTCGCTATGAACTA 58.316 33.333 0.00 0.00 35.97 2.24
821 823 7.548097 TCTTTGTAGAGATTTCGCTATGAACT 58.452 34.615 0.00 0.00 35.97 3.01
822 824 7.757097 TCTTTGTAGAGATTTCGCTATGAAC 57.243 36.000 0.00 0.00 35.97 3.18
823 825 8.948631 AATCTTTGTAGAGATTTCGCTATGAA 57.051 30.769 0.00 0.00 42.24 2.57
840 842 9.338622 CCTCCGTTCCTAAATATAAATCTTTGT 57.661 33.333 0.00 0.00 0.00 2.83
841 843 9.555727 TCCTCCGTTCCTAAATATAAATCTTTG 57.444 33.333 0.00 0.00 0.00 2.77
843 845 9.780186 CTTCCTCCGTTCCTAAATATAAATCTT 57.220 33.333 0.00 0.00 0.00 2.40
844 846 8.935741 ACTTCCTCCGTTCCTAAATATAAATCT 58.064 33.333 0.00 0.00 0.00 2.40
846 848 9.993454 GTACTTCCTCCGTTCCTAAATATAAAT 57.007 33.333 0.00 0.00 0.00 1.40
847 849 8.980596 TGTACTTCCTCCGTTCCTAAATATAAA 58.019 33.333 0.00 0.00 0.00 1.40
848 850 8.537728 TGTACTTCCTCCGTTCCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
849 851 8.716674 ATGTACTTCCTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
850 852 7.613551 ATGTACTTCCTCCGTTCCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
851 853 7.427989 AATGTACTTCCTCCGTTCCTAAATA 57.572 36.000 0.00 0.00 0.00 1.40
852 854 5.952347 ATGTACTTCCTCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
853 855 5.750352 AATGTACTTCCTCCGTTCCTAAA 57.250 39.130 0.00 0.00 0.00 1.85
854 856 8.537728 TTATAATGTACTTCCTCCGTTCCTAA 57.462 34.615 0.00 0.00 0.00 2.69
855 857 8.537728 TTTATAATGTACTTCCTCCGTTCCTA 57.462 34.615 0.00 0.00 0.00 2.94
856 858 7.427989 TTTATAATGTACTTCCTCCGTTCCT 57.572 36.000 0.00 0.00 0.00 3.36
857 859 7.387122 GGATTTATAATGTACTTCCTCCGTTCC 59.613 40.741 0.00 0.00 0.00 3.62
858 860 8.148999 AGGATTTATAATGTACTTCCTCCGTTC 58.851 37.037 0.00 0.00 0.00 3.95
859 861 8.030913 AGGATTTATAATGTACTTCCTCCGTT 57.969 34.615 0.00 0.00 0.00 4.44
860 862 7.613551 AGGATTTATAATGTACTTCCTCCGT 57.386 36.000 0.00 0.00 0.00 4.69
861 863 7.754027 CGTAGGATTTATAATGTACTTCCTCCG 59.246 40.741 0.00 0.00 34.17 4.63
862 864 8.983307 CGTAGGATTTATAATGTACTTCCTCC 57.017 38.462 0.00 0.00 34.17 4.30
906 908 2.282407 GCAATGGCCAATTTGGATGAC 58.718 47.619 19.76 6.31 40.96 3.06
959 965 2.368875 TCTCTGAGTTGTGGGTTTCCTC 59.631 50.000 4.32 0.00 0.00 3.71
973 979 0.967887 TCCGTGAAGCCCTCTCTGAG 60.968 60.000 0.00 0.00 0.00 3.35
985 991 7.223260 AGGACGACATTAATATATCCGTGAA 57.777 36.000 0.00 0.00 0.00 3.18
986 992 6.402875 CGAGGACGACATTAATATATCCGTGA 60.403 42.308 0.00 0.00 42.66 4.35
998 1004 2.414994 AGGAGACGAGGACGACATTA 57.585 50.000 0.00 0.00 42.66 1.90
1272 1281 4.742201 GAGCCGACGCAGAAGCCA 62.742 66.667 0.00 0.00 37.52 4.75
1282 1291 1.142097 GCAAGGAGTAGGAGCCGAC 59.858 63.158 0.00 0.00 0.00 4.79
1617 1656 3.882025 GGCTCAGCCGAGAACAAG 58.118 61.111 0.00 0.00 42.34 3.16
1635 1674 1.873591 GTGTCCAATTCTGACTGCGTT 59.126 47.619 6.28 0.00 33.83 4.84
1647 1686 2.358247 GTGTCCGGCGTGTCCAAT 60.358 61.111 6.01 0.00 34.01 3.16
1648 1687 4.612412 GGTGTCCGGCGTGTCCAA 62.612 66.667 6.01 0.00 34.01 3.53
1854 1893 2.109799 ATGGCCTTCATCCGCTCG 59.890 61.111 3.32 0.00 0.00 5.03
2001 2052 3.282745 GACGAGCACTCAAGCCGGA 62.283 63.158 5.05 0.00 34.16 5.14
2064 2116 5.396772 CCTCTCACCATATGCAAAGGTTAGA 60.397 44.000 14.78 14.78 34.29 2.10
2065 2117 4.818546 CCTCTCACCATATGCAAAGGTTAG 59.181 45.833 5.45 7.64 32.15 2.34
2066 2118 4.227300 ACCTCTCACCATATGCAAAGGTTA 59.773 41.667 5.45 0.00 33.08 2.85
2078 2130 2.614259 AGTCACTCAACCTCTCACCAT 58.386 47.619 0.00 0.00 0.00 3.55
2100 2152 2.932614 CGTGAGCTATGCTTAACAGCTT 59.067 45.455 0.00 0.00 45.42 3.74
2103 2155 3.484229 GCAACGTGAGCTATGCTTAACAG 60.484 47.826 6.04 0.00 39.88 3.16
2104 2156 2.415168 GCAACGTGAGCTATGCTTAACA 59.585 45.455 6.04 0.00 39.88 2.41
2105 2157 2.223044 GGCAACGTGAGCTATGCTTAAC 60.223 50.000 12.28 0.00 39.88 2.01
2106 2158 2.006888 GGCAACGTGAGCTATGCTTAA 58.993 47.619 12.28 0.00 39.88 1.85
2107 2159 1.066502 TGGCAACGTGAGCTATGCTTA 60.067 47.619 12.28 0.00 38.41 3.09
2108 2160 0.321564 TGGCAACGTGAGCTATGCTT 60.322 50.000 12.28 0.00 38.41 3.91
2139 2191 1.922545 GGTAACGTGAACTATGCCGTC 59.077 52.381 0.00 0.00 32.30 4.79
2160 2212 3.389002 GGCTCAATTATTCCTTGCCCAAT 59.611 43.478 0.00 0.00 33.45 3.16
2179 2231 1.898574 CTGGAACAAACTGCGGGCT 60.899 57.895 0.00 0.00 38.70 5.19
2180 2232 2.644992 CTGGAACAAACTGCGGGC 59.355 61.111 0.00 0.00 38.70 6.13
2181 2233 1.733402 TTGCTGGAACAAACTGCGGG 61.733 55.000 0.00 0.00 38.70 6.13
2182 2234 0.314935 ATTGCTGGAACAAACTGCGG 59.685 50.000 0.00 0.00 38.70 5.69
2183 2235 2.138596 AATTGCTGGAACAAACTGCG 57.861 45.000 0.00 0.00 38.70 5.18
2184 2236 3.197265 ACAAATTGCTGGAACAAACTGC 58.803 40.909 0.00 0.00 38.70 4.40
2185 2237 3.803778 GGACAAATTGCTGGAACAAACTG 59.196 43.478 0.00 0.00 38.70 3.16
2186 2238 3.450457 TGGACAAATTGCTGGAACAAACT 59.550 39.130 0.00 0.00 38.70 2.66
2187 2239 3.791245 TGGACAAATTGCTGGAACAAAC 58.209 40.909 0.00 0.00 38.70 2.93
2188 2240 4.478206 TTGGACAAATTGCTGGAACAAA 57.522 36.364 0.00 0.00 38.70 2.83
2192 2244 7.002250 TCAATATTTGGACAAATTGCTGGAA 57.998 32.000 14.68 0.00 40.99 3.53
2202 4082 8.648698 TGGAGAAAAGATCAATATTTGGACAA 57.351 30.769 0.00 0.00 0.00 3.18
2274 4154 9.658799 CATCTTATGTATGGTAGAGTATTTGGG 57.341 37.037 0.00 0.00 0.00 4.12
2286 4166 5.227593 AGAAGGGGTCATCTTATGTATGGT 58.772 41.667 0.00 0.00 0.00 3.55
2318 4198 5.187967 ACCCTACAGGAGACATCTTAAACTG 59.812 44.000 0.00 0.00 39.89 3.16
2320 4200 5.678955 ACCCTACAGGAGACATCTTAAAC 57.321 43.478 0.00 0.00 39.89 2.01
2336 4216 6.760298 GTGTTAAGAGCAAGGTATTACCCTAC 59.240 42.308 9.31 0.00 39.75 3.18
2338 4218 5.487845 AGTGTTAAGAGCAAGGTATTACCCT 59.512 40.000 9.31 0.00 39.75 4.34
2361 4241 1.013596 TGGTTCTTTGTGTGCACGAG 58.986 50.000 13.13 7.61 0.00 4.18
2363 4243 2.548057 ACTATGGTTCTTTGTGTGCACG 59.452 45.455 13.13 0.00 0.00 5.34
2421 4301 5.305386 TCTGAGATCCAGAGTTTCAACTTGA 59.695 40.000 9.14 0.00 46.38 3.02
2523 4403 2.971261 GCACGAGGCTAAAAAGAAAACG 59.029 45.455 0.00 0.00 40.25 3.60
2531 4411 2.048970 TCGCGCACGAGGCTAAAA 60.049 55.556 8.75 0.00 45.12 1.52
2557 4437 1.444383 GCAGAGCGTGTGTGATCGA 60.444 57.895 0.00 0.00 0.00 3.59
2616 4497 6.918626 TGCCATACAATTTTCTTCATCGAAA 58.081 32.000 0.00 0.00 0.00 3.46
2680 4562 5.982890 AATGGGTCATGGAACTTTTACAG 57.017 39.130 0.00 0.00 0.00 2.74
2767 4678 9.814899 ATTATTCGATATGAAATTGGCAAACAA 57.185 25.926 3.01 0.00 40.71 2.83
2768 4679 9.814899 AATTATTCGATATGAAATTGGCAAACA 57.185 25.926 3.01 5.80 40.71 2.83
2770 4681 9.814899 ACAATTATTCGATATGAAATTGGCAAA 57.185 25.926 3.01 0.00 38.36 3.68
2771 4682 9.814899 AACAATTATTCGATATGAAATTGGCAA 57.185 25.926 0.68 0.68 38.36 4.52
2772 4683 9.814899 AAACAATTATTCGATATGAAATTGGCA 57.185 25.926 16.16 0.00 38.36 4.92
2776 4687 9.814899 TGGCAAACAATTATTCGATATGAAATT 57.185 25.926 0.00 0.00 40.71 1.82
2777 4688 9.814899 TTGGCAAACAATTATTCGATATGAAAT 57.185 25.926 0.00 0.00 35.48 2.17
2846 4784 9.327628 TGTACTGTGTTGTTTTTATGTAGCTAA 57.672 29.630 0.00 0.00 0.00 3.09
2856 4794 9.231297 AGCTATATGATGTACTGTGTTGTTTTT 57.769 29.630 0.00 0.00 0.00 1.94
2955 4893 3.349022 AGTAGAGGTGGAGAAGACGAAG 58.651 50.000 0.00 0.00 0.00 3.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.